Proteomic Biomarkers In Drug Development

Biomarker (noun): Biomarkers are cellular, biochemical, or molecular alterations that are measurable in biological media such as human tissues, cells, or fluids. They indicate the presence of biological events or concerted events that are directly associated with a particular disease state.

Molecular Biomarkers (noun): Molecular biomarkers include proteins, carbohydrates, nucleic acids, and other compounds that provide insight into an individual’s health for screening risk factors, diagnosis, and prognosis. Molecular biomarkers are also extremely useful for drug discovery purposes.

Clinical Needs, Patient Perspective:
Am I at risk for cancer?
Is there anything I can do to alter the risk?
Do I have cancer?
Will my cancer respond to therapy?
Is my cancer responding to therapy?

Clinical Needs, Physician Perspective:
Identification of fingerprints associated with:

Prognosis at the time of diagnosis

Tumor responsiveness to therapy

Inter- and intratumor heterogeneity

Metastatic potential

Disease progression

CONTINUED: See Full PDF Document: Proteomic Biomarkers In Drug Development


Conclusions:
The study demonstrated efficacy of IND#70190 with overall improved performance scores and alleviation of asthma symptoms

Novel protein biomarkers for asthma and drug efficacy were identified

Drug effects are consistent with potent anti-inflammatory activity of IND#70190

Further clinical development and investigation of drug mechanism of action is warranted

Novel serum biomarkers for renal cell carcinoma NIH AACR

Background: Renal cell carcinoma (RCC) is often undetected until it is in an advanced stage. Currently there are no reliable blood biomarkers to monitor the presence of the disease and/or response to therapies. Mass spectrometry (MS)-based proteomics provides tools for sensitive and high-throughput screening of proteinaceous biological samples and greatly facilitates biomarker iscovery.

Materials and methods: Sera from patients diagnosed with RCC were obtained at the baseline (n=14), then from the same individuals at 1 week (n=10), 2 weeks (n=5), and 3 weeks (n=7) after radical nephrectomy. In addition, unrelated RCC (n=4) and healthy control sera (n=30) were collected. Levels of inflammatory cytokines and growth factors (interleukins 1β, IL 2-7, 10, 12, and 13, GM-CSF, interferon-γ, TNF-α) were quantified in multiplex immunoassays. SELDI TOF MS protein profiling of the whole sera and specimens immunoprecipitated with anti-kallikrein antibodies was done in IMAC-Cu arrays. Further purification and identification of differentially expressed proteins was achieved by combination of two-dimensional gel electrophoresis (2DPAGE), in-gel trypsin digestion and LC-ESIMS for peptide fingerprinting. LC-ESIMS/MS was then used for de novo peptide sequence analysis. Mass spectral data were reduced using the Mascot database search engine. Initial matches were refined and confirmed against raw data and searched against decoy databases to reinforce identifications. Data were further refined using Progenesis Stats.

Results: Serum levels of all growth factors and cytokines (except IL-6) increased above the baseline until 3 weeks post-nephrectomy, with significant (p<0.05)>

Conclusions: SAA, an inflammatory acute phase protein, has been viewed as a biomarker of host response in many human cancers. The recently reported presence of SAA in tumor tissue suggests alternative function of the protein. Sudden disappearance of SAA versus persistent upregulation of multiple inflammatory proteins in post-nephrectomy RCC sera supports this notion. The additional matches derived from the 2D gels of the immunoprecipitates are all either reasonably expected or supported by recent literature identifications in other pathologies. The identifications of the other targets are being confirmed by independent methods. Selective proteome isolation by targeted MS is a promising analytical tool with potential clinical applications.

Identification of Serum Biomarkers for Lung Cancer

Background: Symptoms of lung cancer (LC) often do not appear until the disease is advanced; only 15% of LC cases are discovered while the tumor is in the early stages of development. Carcinogen exposure, asthma and smoking have been determined to be risk factors for the development of LC. Early detection of LC will likely have a major impact on the natural history of the disease and facilitate curative treatment. The objective of this study was to apply multiplexed immunoassays to identify a panel of biomarkers for early detection of LC.

Methods: Normal (NO) serum controls (n = 30) from healthy volunteers and lung cancer patients (n = 30) were acquired from a commercial vendor. Baseline (pre-treatment) serum specimens from individuals with asthma (AST; n = 28) and lung cancer risk (LCR; n = 73) were available from clinical trials of two novel agents that are being developed by JBNI Inc. for the respective indications. Serum levels of 59 cytokines, growth factors and biologically active peptides were quantified using multiplexed immunoassays using the Luminex platform to identify biomarkers that are expressed in a significantly different manner in individuals with LC, LCR, or AST in comparison with NO subjects. Data were reduced using nearest neighbor cluster analysis with squared Euclidian distance to separate patients into groups across analytes with inter-pathology comparisons determined using Student’s t test.

Results: Multiple analytes showed highly significant differences (p < 0.0002) between LC and healthy controls as single indices of pathologic state. In addition we were able to differentiate AST from LC (p < 0.002) and LCR and LC (p < 0.0001) using a panel of thirteen markers in various combinations. Using multiplexed assays we found significant differences in biomarker levels in sera of LC compared to NO, in NO compared to AST and LC compared to AST samples. Our results support an extended multiplexed immunoassay-based analysis of serum biomarker profiles as supplementary tools for the diagnosis of pathologic and as an aid in the development of novel agents for prevention, early detection and treatment of LC.

Conclusions: We have identified a group of markers having high inter-pathology discrimination power that are capable of reliably differentiating AST and LC from control specimens. This panel remains to be validated in a larger set of specimens but we are confident that these measures will produce clinical assays capable of reliably diagnosing lung pathology.

16th EORTC-NCI-AACR Symposium on Molecular Targets, Cancer Therapeutics

28 September - 1 October 2004, Geneva, Switzerland

Abstracts

Abstract 583: Serum proteomic biomarkers of a natural product in a prospective randomized placebo-controlled clinical trial in patients at risk for lung cancer

Citation: European Journal of Cancer Supplements Volume 2, No.8, September 2004, page 177

S. Baek, D. Campos, E. Izbicka, J Jiang

Cancer Therapy and Research Center, The Institute for Drug Development, San Antonio, TX, USA

Smoking, asthma, and chronic obstructive pulmonary disease (COPD) are known risk factors for lung cancer. The disease may be preventable, but many potential chemopreventive agents have not shown clinical activity in individuals at risk for lung cancer (Van Zandvijk et al, Lung Cancer 2003, 42:S71). A novel natural product LP01 demonstrated preclinical preventive and anticancer activities, and induced time-and dose-dependent changes in serum kallikreins and proteomic patterns in human lung cancer xenograft models (Baek et al, Proc AACR/NCI/EORTC 2003).

The present study evaluated LP01 in a prospective, randomized, triple-masked, placebo-controlled, parallel-group clinical trial. In this study, lung cancer risk (1­5) was assessed based on length of addiction, asthma, and COPD, for a group of former long-term smokers (smoked >20 years, quit >1 year). This group, comprised of sixty men and women ages 35­70, received oral daily doses of 3,650 mg LP01 or placebo for 6 months.

Peripheral blood serum specimens were obtained at the baseline and after drug treatment for 2 weeks, 1 month, 2 months, 4 and 6 months. Serum proteins were resolved on IMAC3/Cu metal affinity ProteinChip arrays and analyzed by surface-enhanced ligand desorption/ionization (SELDI). There were no adverse clinical effects of the therapy. The patients were stratified by the low risk (1 to -

QIFT and PIFT from JBNI

JBNI has been leading the world in cancer prevention research for over a decade. JBNI's presentations on "Cancer Forecasting Proteomics" have been most highly regarded in every international conferences sponsored by NIH (National Institute of Health), NCI ((National Cancer Institute), AACR ( American Association for Cancer Research) and EORTC(European Organization for Research and Treatment of Cancer). JBNI's philosophy and technology in prevention has already gone beyond the wildest expectation of modern world. PIFT (Proteomic Illness Forecasting Test) will "forecast" each individual's cancer and common illnesses years before their earliest stage, which gives everyone many years to prevent such conditions safely with natural modalities. QIFT (Quarterly Illness Forecasting Test) will eliminate the guess work on efficacy of your natural modalities. You will be able to monitor your healthy future precisely and adjust your life style to improve and extend your life. JBNI believes that Homo Sapiens' learning through physical struggle should end, and that new humanity, Homo Sanctus, will advance through polishing of mind.

also check www.aacr.org / www.eortc.org / www.nih.gov / www.cancer.gov / www.ctrc.org / www.idd.org

Renal Cell Carcinoma

Renal cell carcinoma (RCC) is often undetected until it is in an advanced stage. Currently there are no reliable blood biomarkers to monitor the presence of the disease and/or response to therapies. Mass spectrometry (MS)-based proteomics provides tools for sensitive and high-throughput protein screening of biological samples and biomarker discovery.

SAA, an inflammatory acute phase protein, has been viewed as a biomarker of host response in many human cancers. The recently reported presence of SAA in tumor tissue suggests alternative function of the protein. Sudden disappearance of SAA versus persistent upregulation of multiple inflammatory proteins in post-nephrectomy RCC sera supports this notion. Selective proteome isolation by targeted MS is a promising analytical tool with potential clinical applications.

Historical Breakthrough in Treatment of Asthma

JBNI has received an FDA Investigational New Drug Number for our novel natural drug for chronic and debilitating Asthma. This is the first in a line of comprehensive natural, efficacious therapies for chronic medical conditions. Results of our research conducted in conjunction with CTRC Institute for Drug Development, San Antonio, TX, were presented in an abstract entitled "Efficacy, short-term safety, and serum biomarkers in a clinical trial of IND#70190" at the San Antonio Cancer Institute by Dr. Elzbieta Izbicka, chief investigator.
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A Proteomics Victory Over Cancer

04/14/07: Latest RCC Abstract

06/14/06: Our latest abstract

July 2005 our research in the battle against cancer won recognition in the scientific and pharmaceutical community to the extent that we have been presented on the cover of the July-August issue of " Cancer Genomics & Proteomics" , a journal published by the International Institute of Anticancer Research.

Novel natural products LP-01 and LP-02 developed by JBNI, were presented in cooperation with CTRC The Institute for Drug Development, San Antonio, TX at AACR-NCI-EORTC 2004: September 28-October 1, Geneva, Switzerland The AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics, Discovery, Biology, and Clinical Applications was held in Geneva, Switzerland this past September. Our abstract on Serum Proteomic Biomarkers of a Natural Product in a Prospective Randomized Placebo-Controlled Clinical Trial in patients at risk for lung cancer was presented to the acclaim of the attendees.

In November of 2003, at the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics, Discovery Biology, and Clinical Applications held in Boston, Massachusetts, an abstract entitled "Serum Biomarkers of Natural Product Therapy in Human Lung Cancer Xenograft Models" was presented, demonstrating the efficacy of our novel entities (LP-01 and LP-02) in high-risk lung cancer patients.

read our report on Novel serum biomarkers for renal cell carcinoma